Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 25-Oct-2020 from the annotated genome of Acinetobacter sp. Ver3 Ver3, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JFYL0100000116015613161,693RefSeq:NZ_JFYL01000001
NZ_JFYL0100000211311012135,536RefSeq:NZ_JFYL01000002
NZ_JFYL01000003999621104,826RefSeq:NZ_JFYL01000003
NZ_JFYL010000041121071499,489RefSeq:NZ_JFYL01000004
NZ_JFYL0100000599990093,912RefSeq:NZ_JFYL01000005
NZ_JFYL010000061071034093,749RefSeq:NZ_JFYL01000006
NZ_JFYL0100000780780288,181RefSeq:NZ_JFYL01000007
NZ_JFYL0100000889880178,250RefSeq:NZ_JFYL01000008
NZ_JFYL0100000967651176,020RefSeq:NZ_JFYL01000009
NZ_JFYL0100001071691169,310RefSeq:NZ_JFYL01000010
NZ_JFYL0100001149490064,633RefSeq:NZ_JFYL01000011
NZ_JFYL0100001256531261,605RefSeq:NZ_JFYL01000012
NZ_JFYL0100001359535161,189RefSeq:NZ_JFYL01000013
NZ_JFYL0100001447470057,141RefSeq:NZ_JFYL01000014
NZ_JFYL0100001577732254,404RefSeq:NZ_JFYL01000015
NZ_JFYL0100001650481153,750RefSeq:NZ_JFYL01000016
NZ_JFYL0100001743421051,193RefSeq:NZ_JFYL01000017
NZ_JFYL0100001850490149,117RefSeq:NZ_JFYL01000018
NZ_JFYL0100001937370044,152RefSeq:NZ_JFYL01000019
NZ_JFYL0100002049480144,005RefSeq:NZ_JFYL01000020
NZ_JFYL0100002140344243,300RefSeq:NZ_JFYL01000021
NZ_JFYL0100002237343042,327RefSeq:NZ_JFYL01000022
NZ_JFYL0100002342374141,189RefSeq:NZ_JFYL01000023
NZ_JFYL0100002435350040,279RefSeq:NZ_JFYL01000024
NZ_JFYL0100002531310037,667RefSeq:NZ_JFYL01000025
NZ_JFYL0100002643411137,559RefSeq:NZ_JFYL01000026
NZ_JFYL0100002735340137,324RefSeq:NZ_JFYL01000027
NZ_JFYL0100002832290336,533RefSeq:NZ_JFYL01000028
NZ_JFYL0100002931310036,268RefSeq:NZ_JFYL01000029
NZ_JFYL0100003029260336,232RefSeq:NZ_JFYL01000030
NZ_JFYL0100003148415236,162RefSeq:NZ_JFYL01000031
NZ_JFYL0100003235303234,790RefSeq:NZ_JFYL01000032
NZ_JFYL0100003327270033,518RefSeq:NZ_JFYL01000033
NZ_JFYL0100003434340032,199RefSeq:NZ_JFYL01000034
NZ_JFYL0100003527260132,039RefSeq:NZ_JFYL01000035
NZ_JFYL0100003631274030,751RefSeq:NZ_JFYL01000036
NZ_JFYL0100003723171530,572RefSeq:NZ_JFYL01000037
NZ_JFYL0100003827241230,136RefSeq:NZ_JFYL01000038
NZ_JFYL0100003928270129,146RefSeq:NZ_JFYL01000039
NZ_JFYL0100004023221029,114RefSeq:NZ_JFYL01000040
NZ_JFYL0100004131300128,191RefSeq:NZ_JFYL01000041
NZ_JFYL0100004229290026,301RefSeq:NZ_JFYL01000042
NZ_JFYL0100004325212225,502RefSeq:NZ_JFYL01000043
NZ_JFYL0100004426170924,649RefSeq:NZ_JFYL01000044
NZ_JFYL0100004522220024,437RefSeq:NZ_JFYL01000045
NZ_JFYL0100004619190024,095RefSeq:NZ_JFYL01000046
NZ_JFYL0100004722220022,937RefSeq:NZ_JFYL01000047
NZ_JFYL0100004816150120,048RefSeq:NZ_JFYL01000048
NZ_JFYL0100004919170220,040RefSeq:NZ_JFYL01000049
NZ_JFYL0100005022220019,941RefSeq:NZ_JFYL01000050
NZ_JFYL0100005118180019,762RefSeq:NZ_JFYL01000051
NZ_JFYL0100005220180218,983RefSeq:NZ_JFYL01000052
NZ_JFYL0100005315140118,723RefSeq:NZ_JFYL01000053
NZ_JFYL0100005418162018,217RefSeq:NZ_JFYL01000054
NZ_JFYL0100005521180318,194RefSeq:NZ_JFYL01000055
NZ_JFYL0100005614140017,785RefSeq:NZ_JFYL01000056
NZ_JFYL0100005721180317,530RefSeq:NZ_JFYL01000057
NZ_JFYL0100005818180017,251RefSeq:NZ_JFYL01000058
NZ_JFYL0100005918170116,575RefSeq:NZ_JFYL01000059
NZ_JFYL0100006013120116,061RefSeq:NZ_JFYL01000060
NZ_JFYL0100006117142115,926RefSeq:NZ_JFYL01000061
NZ_JFYL0100006215150015,875RefSeq:NZ_JFYL01000062
NZ_JFYL0100006316140214,982RefSeq:NZ_JFYL01000063
NZ_JFYL0100006413130014,697RefSeq:NZ_JFYL01000064
NZ_JFYL0100006512120014,360RefSeq:NZ_JFYL01000065
NZ_JFYL0100006613120114,226RefSeq:NZ_JFYL01000066
NZ_JFYL0100006717150213,880RefSeq:NZ_JFYL01000067
NZ_JFYL0100006914130113,562RefSeq:NZ_JFYL01000069
NZ_JFYL0100007013110213,468RefSeq:NZ_JFYL01000070
NZ_JFYL0100007117170013,334RefSeq:NZ_JFYL01000071
NZ_JFYL010000721280413,115RefSeq:NZ_JFYL01000072
NZ_JFYL0100007312111012,609RefSeq:NZ_JFYL01000073
NZ_JFYL0100007413130012,595RefSeq:NZ_JFYL01000074
NZ_JFYL0100007515140112,417RefSeq:NZ_JFYL01000075
NZ_JFYL0100007613130012,404RefSeq:NZ_JFYL01000076
NZ_JFYL0100007714113011,745RefSeq:NZ_JFYL01000077
NZ_JFYL0100007812110111,515RefSeq:NZ_JFYL01000078
NZ_JFYL0100008011110011,165RefSeq:NZ_JFYL01000080
NZ_JFYL010000871212009,949RefSeq:NZ_JFYL01000087
NZ_JFYL010000891212009,803RefSeq:NZ_JFYL01000089
NZ_JFYL010000911212009,599RefSeq:NZ_JFYL01000091
128 Undisplayed Contigs/Replicons2922801262409,591
Total:3,2182,998701503,345,299
Ortholog data available?Yes
Database Contents
Genes3,218
Pathways245
Enzymatic Reactions1,181
Transport Reactions70
Polypeptides3,095
Protein Complexes38
Enzymes710
Transporters293
Compounds864
Transcription Units2,293
tRNAs62
Protein Features3,698
GO Terms14,001
Database Version29.0
Sequence SourceGCF_000632455.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
unclassified Acinetobacter
Acinetobacter sp. Ver3
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02678190
NCBI BioProjectPRJNA224116
NCBI-Taxonomy466088
EnvironmentLake surface
Geographic LocationArgentina
Latitude/Longitude27.655603 S 68.64693 W
Depth (m)-5.0
Collection Date2006-11-20
Relationship to Oxygenaerobe
Trophic Levelorganoheterotroph
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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